Nucleic acids, either DNA or RNA, single-stranded or double-stranded, are the most fundamental and important class of biomolecules in a living cell. DNA encodes the genetic information that passes from generation to generation. Through transcription, the coded information is transferred to mRNA, which binds to ribosome (specific ribosomal RNA and protein complex). With the assistance of tRNA, which contains an anticodon and a specific amino acid, the carried information of mRNA is translated into a precise sequence of a polypeptide of 20 amino acids. Folding of the polypeptide into a well-defined three-dimensional structure gives rise to a protein. Many classes of proteins act as building blocks, enzymes, and regulation factors. Together with other classes of biomolecules, proteins are responsible for the structure and proper function of a living cell.
Since nucleic acids carry multiple negatively charged phosphate functional groups, they are polyanions. Under physiological conditions, poly(aspartic acid) and poly(glutamic acid) form polycarboxylates, which are also polyanions. On the other hand, polylysine, polyarginine, and polyhistidine (in an acidic aqueous solution) carry multiple positive charges, and are considered polycations. Many proteins, when the solution pH is not at their isoelectric point (pI) value, carry net positive or negative multiple charges (21). In light of the above, methods that can detect and characterize biomolecules with multiple charges are of great importance, which can not only help us to understand how the cell functions, assist biological/biochemical research, but may also provide ways to facilitate biomedical research, clinical diagnosis, and new drug development.
The intriguing structural and bonding properties of square-planar d8 or d10 metal complexes have attracted long-standing interest, and more so recently with the growing interest in the spectroscopic properties associated with this class of metal complexes. These metal complexes are known to display a strong tendency towards the formation of highly-ordered extended linear chains or oligomeric structures in the solid state. The extent of the metal-metal interaction and the π . . . π stacking of the aromatic ligand have led to the observation of interesting spectroscopic and luminescence properties, and recent reports based on the utilization of these observations for molecular recognition, chemosensing, and optoelectronic applications have been made (17, 19, 24, 26-28, 30, 37, 38, 45-48).
A representative example of the class of the aforementioned d8 or d10 metal complexes is the alkynylplatinum(II) terpyridyl complexes (45-47). By changing the solvent polarity, or using a polyelectrolyte, namely polyacrylate (a polyanion), the d8 or d10 metal complexes are induced to aggregate and self-assemble, thereby creating observable dramatic changes in the UV/vis and emission spectra (46, 49). In addition, when the complex was mixed with single-stranded nucleic acid in an aqueous solution, dramatic UV/vis and emission spectral changes were also observed; the spectral changes were closely related to the structure of the single-stranded nucleic acid as well as the structural properties of the complex (50).
There are a number of assay methods available nowadays for the detection and characterization of multiple-charged biomolecules. However, most of the commonly used existing methods require sophisticated analytical techniques and expensive instrumentation. Many of these methods require labeling with a detectable group, which can be a radioisotope or a fluorescent substance, as well as hybridization procedures for nucleic acid detection. Hence, such methods usually demand high financial cost and are technically complicated and time-consuming.
The importance of our metal complex self-assembly related bio-sensing technology invention can be further illustrated by the following important areas of nucleic acid sensing related research that have been under our extensive investigation.
One important class of nucleic acid is telomeric DNA, which is located at the end of linear eukaryotic chromosomes, and consists of simple tandem repeats of guanine-rich sequences. The majority of telomeric DNA is double-stranded, but the extreme 3′ ends are single-stranded, which have the propensity to form four-stranded structures known as G-quadruplexes (18, 20). A guanine quartet is composed of four coplanar guanine nucleobases, stabilized by cyclic Hoogsteen hydrogen bonding, and also by coordination of carbonyl oxygen of guanine with monovalent cations, such as sodium or potassium (FIG. 1). Several quartets stack on top of each other to form G-quadruplex. The enzyme telomerase, a ribonucleoprotein, is a reverse transcriptase. It acts to extend the telomere length, and is inactive in normal human somatic cells, but active in 85-90% of cancer cells. Formation and stabilization of G-quadruplex structure at telomere ends can inhibit telomerase activity, and such strategy has been a very active area of anti-cancer research (25, 33, 35, 43, 44).
In addition, since G-quadruplex formation is stabilized by monovalent cations, it can also be used to selectively sense the presence of potassium ion. Potassium ion (K+) plays an important role in biological systems together with sodium, calcium, magnesium, and other metal ions. Therefore the development of a method to specifically detect potassium ion in a cell is very important.
An important aspect of potassium ion sensing is related to hERG, which is a potassium ion channel. In the late 1990s a number of drugs, approved by the FDA (U.S. Department of Health and Human Services Food and Drug Administration) and available on the market, had to be withdrawn from sales in the US when it was discovered that they were implicated in deaths caused by heart malfunction. It is now known that a side effect of these drugs was the blocking of hERG channels in heart cells. This caused prolongation of action potentials, which are the electrical pulses responsible for controlling heart muscle cells. With the proper control of the rate of heartbeat lost, dangerous arrhythmias could develop, which leads in some cases to death.
An unbalanced K+ concentration is associated with the onset of irregular heartbeat and hERG-blocking properties can end the prospects for a potential drug. However, there is now no simple way to predict how the structure of a drug would determine whether it will block hERG or not. Therefore, testing on these channels needs to be implemented early in the drug-screening procedure. In many companies all drug candidates will be tested for hERG blocking before any further investigation is carried out since there is no point in going on with a compound that can never get into the market. The enormous number of compounds that need to be screened and tested will provide a formidable challenge to pharmaceutical companies. Thus the development of an efficient high throughput assay that is simple, easy to operate and without the need of the talents of highly trained and creative scientists is important. Real-time monitoring of the extracellular concentration of K+ ions (2-10 mM) would require the indicator to exhibit a sufficiently high response in the presence of a complex matrix containing several ions (Na+, Mg2+, Ca2+, and Cl−) at millimolar concentrations. Thus the challenge will be to develop an assay that can sense selectively K+ ions in the presence of other metal ions, in particular the Na+ and Ca2+ ions, as K+ ion plays an important role in biological systems together with Na+, Mg2+, Ca2+, and other metal ions. At present, the high throughput assay adopted for drug-screening is using Rb as the potassium analogue. Development of a simple real-time assay of stimulated K+ efflux from cells will have the potential to supplement or replace 86Rb efflux measurements (29, 31, 32, 34, 41, 42).
Recently, selective and sensitive K+ assays based on G-quadruplex forming oligonucleotides have been reported, as G-quadruplex has a channel at its center with a diameter that correlates well with the ionic radius of K+(1.3 Å). However, these works are mostly based on the dual-labeling of oligonucleotide derivatives with donor and acceptor dyes for fluorescence resonance energy transfer (FRET) and quenching assays (40, 52), involving rather tedious labeling procedures. A related pyrene-labeled oligonucleotide has been developed for selective potassium ion sensing based on excimer emission upon G-quadruplex formation (39), which can be potentially exploited for the real-time monitoring of K+ ions under extracellular conditions. The greater selectivity of these systems towards K+ ions over Na+ ions have made the exploitation of G-quadruplex forming oligonucleotides attractive. However, the involvement of tedious labeling techniques represents a major drawback in these systems. The present assay, which involves a simple label-free method and does not require the tedious labeling or tethering of the platinum(II) indicator via covalent bonding to the G-rich oligonucleotides, is advantageous and is superior to other commonly employed methods, and may be explored for real-time monitoring purposes.
The cleavage of DNA by nuclease such as restriction endonuclease and nonspecific nuclease is involved in many important biological processes, such as DNA replication, recombination, and repair. Single-stranded nucleic acid specific nuclease has been widely used as a tool in molecular biology, such as removal of nonannealed single-stranded nucleic acid tail, hairpin loop, etc. So far, only a few nuclease assay methods are commonly used, such as gel electrophoresis, high performance liquid chromatography (HPLC), sedimentation, and enzyme linked immunosorbent assay (ELISA). These methods are time-consuming, laborious, and usually require substrate labeling.
It has been well-documented that reactive oxygen species such as the superoxide radical anion, hydrogen peroxide, and the hydroxyl radical cause damage to various biomolecules. DNA damage/cleavage by radical species has drawn much attention in recent years, due to its possible involvement in mutagenesis, carcinogenesis, and apoptosis. DNA damage by hydroxyl radicals generates characteristic mutagenic base damages, and the DNA strand breaks into small fragments. Therefore study of the DNA damage/cleavage is of obvious importance. We envisage that our new technique could be used for in vivo detection of reactive oxygen species.
In summary, the present invention provides a novel label-free assay method to sense and characterize multiple-charged biomolecules. Binding of the charged d8 or d10 metal complex to the biomolecule carrying opposite charges induces aggregation and self-assembly of the metal complex, and hence gives rise to remarkable UV/vis, emission, and CD intensity changes. The assay not only provides a means to detect the presence of multiple-charged biomolecules, to study their secondary structure and structure/conformation changes, selectively sense specific metal ion, but can also be used to study nucleic acid cleavage by nuclease and damage by reactive oxygen species, and thus can be extended for the detection of nuclease and reactive oxygen species.